EMBL Australia PhD students are based in six Australian cities:
- ARC Centre of Excellence in Advanced Molecular Imaging (Imaging CoE), based at Monash University
- Australian Regenerative Medicine Institute (ARMI), based at Monash University
- Single Molecule Science (SMS), based at the University of New South Wales. SMS is also the home of the NSW Node of the ARC Centre of Excellence in Advanced Molecular Imaging
- Garvan Institute of Medical Research, based at the University of New South Wales.
- South Australian Health & Medical Research Institute (SAHMRI) associated with the University of Adelaide, the University of South Australia and Flinders University.
- The John Curtin School of Medical Research at the Australian National University.
- QIMR Berghofer Medical Research Institute, associated with Queensland University of Technology and the University of Queensland, and based in the Royal Brisbane and Women’s Hospital precinct.